xenial (1) macs2_refinepeak.1.gz

NAME

       macs2_refinepeak - Model-based Analysis for ChIP-Sequencing

DESCRIPTION

       usage: macs2 refinepeak [-h] -b BEDFILE -i IFILE [IFILE ...]

       [-f {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}]
              [-c CUTOFF] [-w WINDOWSIZE] [--verbose VERBOSE] [--outdir OUTDIR] (-o OFILE | --o-prefix OPREFIX)

   optional arguments:
       -h, --help
              show this help message and exit

       -b BEDFILE
              Candidate peak file in BED format. REQUIRED.

       -i IFILE [IFILE ...], --ifile IFILE [IFILE ...]
              ChIP-seq alignment file. If multiple files are given as '-t A B C', then they will all be read and
              combined. Note that pair-end data is not supposed to work with this command. REQUIRED.

       -f                    {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE},                    --format
       {AUTO,BAM,SAM,BED,ELAND,ELANDMULTI,ELANDEXPORT,BOWTIE}
              Format of tag file, "AUTO", "BED" or "ELAND" or "ELANDMULTI" or "ELANDEXPORT" or "SAM" or "BAM" or
              "BOWTIE". The default AUTO option will let 'macs2 refinepeak' decide which  format  the  file  is.
              Please      check      the      definition      in      README      file     if     you     choose
              ELAND/ELANDMULTI/ELANDEXPORT/SAM/BAM/BOWTIE. DEFAULT: "AUTO"

       -c CUTOFF, --cutoff CUTOFF
              Cutoff DEFAULT: 5

       -w WINDOWSIZE, --window-size WINDOWSIZE
              Scan window size on both side of the summit (default: 100bp)

       --verbose VERBOSE
              Set verbose level. 0: only show critical message, 1: show  additional  warning  message,  2:  show
              process  information,  3:  show debug messages. If you want to know where are the duplicate reads,
              use 3. DEFAULT:2

       --outdir OUTDIR
              If specified all output files will be written to that  directory.  Default:  the  current  working
              directory

       -o OFILE, --ofile OFILE
              Output file name. Mutually exclusive with --o-prefix.

       --o-prefix OPREFIX
              Output file prefix. Mutually exclusive with -o/--ofile.